Author: Yassine Naimi

In this tutorial, you will learn how to run a simple but powerful technique, called positional analogue scanning, in order to generate new analogs of your molecules directly in SAMSON using the SMILES Manager extension. This new functionality was inspired by this blog post from Pat Walters and this paper from Lewis Pennington, Ingo Muegge, and coworkers. It will allow you to evaluate the effects of newly introduced changes of your molecules on their properties, like the binding affinity (using Autodock Vina Extended SAMSON…

More…

In this tutorial, we will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Extension. This SAMSON Extension computes the nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134). First, you have to import a structure. For this tutorial I used the 1vpk PDB entry. Then, you launch the NMAL module and indicate the desired number of modes,…

More…

In this tutorial, you will learn how to use the SMILES Manager extension of SAMSON. This extension is based on RDKit. RDKit is a widely used open-source toolkit for cheminformatics. One of its features is the conversion of molecules SMILES strings to 2D and 3D structures. The extension interface presents three tabs: Manage SMILES, Replace fragments, and Positional Analogue Scanning. In this tutorial, we will present the first two sections one by one as they are totally independent. For the…

More…

In this tutorial, we will present you the functionalities of the Normal Modes Advanced (NMA) SAMSON Extension. This SAMSON Extension is an advanced version of the Normal Modes Analysis SAMSON Extension also available on SAMSON Connect. This SAMSON Extension computes nonlinear normal modes of a biomolecular system (protein, RNA, DNA) very quickly using the NOLB algorithm developed by Alexandre Hoffmann and Sergei Grudinin (J. Chem. Theory Comput., 2017, 13 (5), pp 2123-2134). First, you have to import a structure. For this…

More…